Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:

  • Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.

  • Frameshift alignments for long read analysis.

  • Low resource requirements and suitable for running on standard desktops or laptops.

  • Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

Detailed about its usage can be found here: https://github.com/bbuchfink/diamond


  • 2.0.13

  • 2.0.14

  • 2.0.15

  • 2.1.6


  • diamond makedb

  • diamond prepdb

  • diamond blastp

  • diamond blastx

  • diamond view

  • diamond version

  • diamond dbinfo

  • diamond help

  • diamond test


You can load the modules by:

module load biocontainers
module load diamond/2.0.14

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run diamond on our our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 24
#SBATCH --job-name=diamond
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers diamond/2.0.14

diamond makedb  --in uniprot_sprot.fasta -d uniprot_sprot
diamond blastp -p 24 -q test.faa -d uniprot_sprot  --very-sensitive -o blastp_output.txt